AMBER Archive (2004)

Subject: Re: AMBER: Periodic boundary simulation

From: Jiten (jiten_at_postech.ac.kr)
Date: Tue Jun 01 2004 - 05:14:59 CDT

Hello,

You can put back the water using ptraj image. And you will see that all the water molecules will be inside the box again.

JIten
  ----- Original Message -----
  From: Soon
  To: amber_at_scripps.edu
  Sent: Tuesday, June 01, 2004 6:08 PM
  Subject: AMBER: Periodic boundary simulation

  Hello all,

  I am using Amber8 and I made octahedron simulation box by

  xx=loadpdb xx.pdb
  Solvateoct xx TIP3PBOX 4

  on leap with ff03 paramters.

  After minimization of the water solvated system, I performed NVT molecular dynamics simulation to equilibrate the system for about 50.0 ps.

  Now, my question is why on earth the water molecules are coming out of the octahedron simulation box during this NVT molecular dynamics run ? As I know the water molecules are suppose to move around inside the simulation box during the MD simulation. Not out of the box.
  The system is not cluster system after all !

  Here is my MD input.

  test
  &cntrl
  ntb=1, ig=33333,
  tempi=300.0, temp0=300.0, ntt=1,
  irest=0, ntx=1,
  nstlim=40000,
  dt=0.0017, ntc=2, cut=9.0,
  ntwe=200, ntwx=200, ntpr=200,
  /

  Am I missing something ? Any comments will be appreciated. Thank you.

  Soon

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